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Check memory CP, turn Virtual Memory off and see if you get your space back when you restart... rebuild the desktop when you restart with VM off, then check size. Another possibility is dying sectors on the HD, but not as likely.

Did she check for invisibles? (using the Custom button on Sherlock, or holding Option in "more options" on the old Find utility. Or get FileBuddy)
What about the TemporaryItems Folder, also invisible, regulary sizable and a pain to get rid of in Sys 9. There is a freeware piece called AutoPurge that will take care of it. I recommend placing it in the Startup Items Folder.
Good luck